Phenotypic Mutation 'cubone' (pdf version)
Allelecubone
Mutation Type splice site
Chromosome15
Coordinate78,330,857 bp (GRCm39)
Base Change A ⇒ T (forward strand)
Gene Tmprss6
Gene Name transmembrane serine protease 6
Synonym(s) matriptase-2, 1300008A22Rik
Chromosomal Location 78,323,867-78,352,834 bp (-) (GRCm39)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a type II transmembrane serine proteinase that is found attached to the cell surface. The encoded protein may be involved in matrix remodeling processes in the liver. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
PHENOTYPE: Homozygosity for an inactivating mutation of this gene results in hair loss over the entire body except the face, microcytic anemia and female infertility, all reversible by dietary iron supplementation. [provided by MGI curators]
Accession Number

NCBI RefSeq: NM_027902; MGI:1919003

MappedYes 
Amino Acid Change
Institutional SourceBeutler Lab
Gene Model predicted gene model for protein(s): [ENSMUSP00000017086 ] [ENSMUSP00000155414 ] [ENSMUSP00000155355 ] [ENSMUSP00000155435] [ENSMUSP00000155549 ] [ENSMUSP00000155401 ]   † probably from a misspliced transcript
AlphaFold Q9DBI0
SMART Domains Protein: ENSMUSP00000017086
Gene: ENSMUSG00000016942

DomainStartEndE-ValueType
low complexity region 19 39 N/A INTRINSIC
transmembrane domain 57 79 N/A INTRINSIC
Pfam:SEA 88 191 3.2e-13 PFAM
CUB 341 452 3.82e-2 SMART
LDLa 457 489 1.33e-2 SMART
LDLa 490 527 2.31e-9 SMART
LDLa 530 568 1.07e-4 SMART
Tryp_SPc 576 806 3.75e-97 SMART
Predicted Effect probably null
Predicted Effect probably null
Predicted Effect probably null
Predicted Effect probably benign
Predicted Effect probably null
Predicted Effect probably null
Meta Mutation Damage Score 0.9755 question?
Is this an essential gene? Probably nonessential (E-score: 0.067) question?
Phenotypic Category Autosomal Recessive
Candidate Explorer Status loading ...
Single pedigree
Linkage Analysis Data
Penetrance  
Alleles Listed at MGI

All Mutations and Alleles(12) : Chemically induced (ENU)(3) Gene trapped(2) Radiation induced(1) Targeted(6)

Lab Alleles
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01066:Tmprss6 APN 15 78326634 missense probably null 1.00
IGL02474:Tmprss6 APN 15 78326536 missense probably damaging 0.99
dilutional UTSW 15 78328328 missense probably damaging 1.00
Ekans UTSW 15 78343627 splice site probably null
mask UTSW 15 78464455 intron probably benign
masquerade UTSW 15 78352200 intron probably benign
zorro UTSW 15 78464552 intron probably benign
BB003:Tmprss6 UTSW 15 78337050 missense probably benign 0.28
BB013:Tmprss6 UTSW 15 78337050 missense probably benign 0.28
PIT1430001:Tmprss6 UTSW 15 78324827 missense probably damaging 1.00
R0285:Tmprss6 UTSW 15 78337068 missense probably damaging 0.99
R1857:Tmprss6 UTSW 15 78336752 missense probably damaging 1.00
R2432:Tmprss6 UTSW 15 78349304 splice site probably benign
R4192:Tmprss6 UTSW 15 78330857 splice site probably null
R4226:Tmprss6 UTSW 15 78330899 missense probably damaging 1.00
R4227:Tmprss6 UTSW 15 78330899 missense probably damaging 1.00
R4334:Tmprss6 UTSW 15 78343627 splice site probably null
R4344:Tmprss6 UTSW 15 78343627 splice site probably null
R4446:Tmprss6 UTSW 15 78337039 missense probably damaging 1.00
R4508:Tmprss6 UTSW 15 78343978 missense probably damaging 1.00
R4643:Tmprss6 UTSW 15 78329556 missense probably damaging 0.98
R4743:Tmprss6 UTSW 15 78327910 missense probably damaging 0.99
R4836:Tmprss6 UTSW 15 78329588 missense probably damaging 1.00
R4859:Tmprss6 UTSW 15 78330877 missense probably damaging 0.99
R4869:Tmprss6 UTSW 15 78327880 splice site probably null
R5197:Tmprss6 UTSW 15 78338389 missense probably damaging 1.00
R5212:Tmprss6 UTSW 15 78330460 missense probably damaging 0.99
R5225:Tmprss6 UTSW 15 78336707 missense probably damaging 0.97
R5569:Tmprss6 UTSW 15 78324503 missense probably damaging 1.00
R5572:Tmprss6 UTSW 15 78326622 missense probably damaging 1.00
R5669:Tmprss6 UTSW 15 78339156 missense possibly damaging 0.86
R5947:Tmprss6 UTSW 15 78336722 missense probably damaging 1.00
R6800:Tmprss6 UTSW 15 78324457 missense probably damaging 1.00
R6941:Tmprss6 UTSW 15 78330977 missense probably damaging 1.00
R6965:Tmprss6 UTSW 15 78328328 missense probably damaging 1.00
R7334:Tmprss6 UTSW 15 78328017 missense unknown
R7338:Tmprss6 UTSW 15 78344019 missense probably damaging 1.00
R7622:Tmprss6 UTSW 15 78330926 missense probably benign 0.40
R7926:Tmprss6 UTSW 15 78337050 missense probably benign 0.28
R7992:Tmprss6 UTSW 15 78326664 missense probably benign 0.11
R8177:Tmprss6 UTSW 15 78349327 missense probably benign 0.01
R8792:Tmprss6 UTSW 15 78328328 missense probably damaging 1.00
R8881:Tmprss6 UTSW 15 78327987 makesense probably null
R9084:Tmprss6 UTSW 15 78338417 missense probably damaging 0.98
R9384:Tmprss6 UTSW 15 78328302 missense probably damaging 0.99
X0025:Tmprss6 UTSW 15 78339295 missense possibly damaging 0.55
Mode of Inheritance Autosomal Recessive
Local Stock
Repository
Last Updated 2019-09-04 9:44 PM by Anne Murray
Record Created 2015-12-03 6:55 AM by Carlos Reyna
Record Posted 2015-12-23
Phenotypic Description
Figure 1. The cubone mice (top) exhibit hair loss and is smaller than their wild-type littermates (bottom).
Figure 2. The cubone mouse exhibits hair loss on the body, but retains hair on the head.

The cubone phenotype was identified among G3 mice of the pedigree R4192, some of which showed hair loss from the trunk; facial hair is preserved in the cubone mice (Figure 1 & 2). In addition, the cubone mice are slightly smaller than their littermates (Figure 1).

Nature of Mutation

Whole exome HiSeq sequencing of the G1 grandsire identified 40 mutations. Among these, only one affected a gene with known effects on hair loss, Tmprss6. The mutation in Tmprss6 was presumed to be causative because the cubone hair loss phenotype mimics other known alleles of Tmprss6 (see MGI for a list of Tmprss6 alleles as well as the mask (1), zorro, and masquerade strains from our lab). The Tmprss6 mutation is a T to A transversion at base pair 78,446,657 (v38) on chromosome 15, or base pair in the GenBank genomic region NC_000081 for the Tmprss6 gene. The mutation is within intron 11, 6-base pairs from the previous exon (exon 11 out of 18 total exons).

 
The effect of the mutation at the cDNA and protein level have not examined, but the mutation is predicted to result in the loss of the splice donor site in intron 11 with a concomitant use of a cryptic splice site in intron 11, leading to a 16-base pair insertion. The insertion would result in an in-frame protein product after amino acid 456 of the TMPRSS6 protein, followed by termination after the inclusion of 811 aberrant amino acids.
 
 
            <--exon 10         <--exon 11 intron 11-->                exon 12-->        <--exon 18
16160 ……ATCCAGAACAGGAG ……TACAACCAATCAGACC gtgagtacaatttgaggtgtgtgtg…… CCTGCCCTGGT…… ……GTGCTGACCTGA…… 28424
404   ……-I--Q--N--R--R ……-Y--N--Q--S--D--                             P--C--P--G-…… ……-V--L--T--*-     811

                    correct                                                     correct

 
 
Genomic numbering corresponds to NC_000084. The donor splice site of intron 11, which is destroyed by the cubone mutation, is indicated in blue lettering, the mutated nucleotide is indicated in red, and the putative cryptic splice site is indicated in green.
Illustration of Mutations in
Gene & Protein
Protein Prediction

Figure 3. Domain structure of TMPRSS6. The C-terminus of the protein, including the serine protease domain, is extracellular. Predicted N-glycosylation sites are noted in violet circles. The cubone mutation is within intron 11. This image is interactive. Click on the image to view other mutations found in TMPRSS6 (red). Click on the mutations for more specific information. 

Tmprss6 encodes an 811-amino acid protein of the type II transmembrane protease family (2). TMPRSS6, also known as matriptase-2, is predicted to contain a C-terminal trypsin-like serine protease domain (shown to be extracellular), three class A LDL receptor domains, two CUB domains (similar to a domain represented in BMP1 as well as C1R and C1S proteins), and a membrane-proximal SEA domain (Figure 3) (1;3)

Please see the record for mask for information about Tmprss6.

Putative Mechanism

The peptide hormone hepcidin, encoded by the Hamp gene, was identified as the major systemic iron regulator (4;5). TMPRSS6 is a non-redundant component in a pathway that senses iron deficiency and negatively regulates Hamp expression to promote iron uptake (1). TMPRSS6 proteolytic activity is critical for its Hamp-suppressing activity. Further study will be required to fully understand the mechanisms by which TMPRSS6 mediates Hamp inhibition and promotes iron uptake. The mechanism of hair loss in Tmprss6-mutant mice, including cubone, remains to be established, although severe iron deficiency is associated with hair loss in humans (6) as in mice (7).

Primers PCR Primer
cubone_pcr_F: GGTCCATGCAGAGCTACATC
cubone_pcr_R: ATGTGTCTAAGCCATCCCTGG

Sequencing Primer
cubone_seq_F: CAAAGGGATACATGTGACTGCCTAC
cubone_seq_R: CTGGTCACTCCTAGGCTGTG
Genotyping

PCR program

1) 94°C 2:00
2) 94°C 0:30
3) 55°C 0:30
4) 72°C 1:00
5) repeat steps (2-4) 40x
6) 72°C 10:00
7) 4°C hold


The following sequence of 400 nucleotides is amplified (chromosome 15, - strand):


1   atgtgtctaa gccatccctg gtcactccta ggctgtgtgg cttccgtacc ctgcagccat
61  atgctgagag gatccccatg gtggcctcag atggtgtcac catcaacttc acctcccaga
121 tctccctcac aggcccgggt gtgcaagtgt actacagctt gtacaaccaa tcagaccgtg
181 agtacaattt gaggtgtgtg tgtgtgtgtg tgtgtgtgcc cgtgccctgc ccctgtgctg
241 tccccagatg tgcacaaaca tttatgaggc taggccacag tgagagtgct atgtgtcttc
301 atacacatgt gtgcacatgg cacgtagttt tatgtgctgg gtaggcagtc acatgtatcc
361 ctttgggtgt gtgttgtctg gatgtagctc tgcatggacc 


Primer binding sites are underlined and the sequencing primers are highlighted; the mutated nucleotide is shown in red.

References
Science Writers Anne Murray
Illustrators Peter Jurek
AuthorsCarlos Reyna, Jamie Russell, and Bruce Beutler